Contacts of the strand formed by residues 587 - 590 (chain P) in PDB entry 1O18


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with THR 587 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    469P  ILE*     4.8     9.5    -      -       -      +
    566P  GLN*     5.7     2.5    +      -       -      +
    574P  LYS*     4.3     5.3    +      -       -      +
    580P  SER*     3.7    26.2    -      -       -      -
    581P  LEU      3.1     8.8    +      -       -      +
    582P  VAL*     4.0    14.5    -      -       +      +
    586P  GLY*     1.3    71.3    -      -       -      -
    588P  VAL*     1.3    68.4    -      -       -      +
    589P  ASP*     4.1    13.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 588 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    467P  PHE*     3.6    36.8    -      -       +      -
    468P  GLU      5.4     0.2    -      -       -      +
    469P  ILE*     4.1    14.6    -      -       +      -
    473P  ASN*     3.5    31.4    -      -       +      +
    481P  ASN*     4.2     6.3    -      -       -      +
    580P  SER*     2.8    25.8    -      -       -      -
    581P  LEU      2.9    13.0    +      -       -      -
    583P  HIS*     3.8     6.5    -      -       +      -
    586P  GLY      4.3     1.6    -      -       -      +
    587P  THR*     1.3    78.1    -      -       -      +
    589P  ASP*     1.3    64.0    +      -       -      +
    590P  TYR*     3.5    33.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 589 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    471P  ASP      4.8     2.3    -      -       -      +
    473P  ASN*     2.9    33.6    +      -       -      +
    568P  PRO*     3.8     7.8    -      -       +      +
    569P  LYS*     3.7    16.9    +      -       -      +
    574P  LYS*     0.6   100.0    +      -       +      +
    576P  GLU      5.5     4.7    -      -       -      +
    579P  PHE      3.9     2.7    -      -       -      -
    580P  SER*     3.4    20.0    +      -       -      -
    587P  THR*     4.3     1.3    -      -       -      +
    588P  VAL*     1.3    73.5    -      -       -      +
    590P  TYR*     1.3    60.8    +      -       -      +
    591P  ASN      4.1     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 590 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    473P  ASN*     3.4    17.5    -      -       +      +
    474P  SER      4.1     7.4    -      -       -      -
    477P  GLN*     4.0     7.0    -      -       +      -
    478P  LEU*     3.4    41.2    -      -       +      +
    481P  ASN*     3.1    16.3    +      -       -      +
    576P  GLU      6.1     0.9    -      -       -      -
    578P  HIS*     3.3    11.3    +      -       -      +
    579P  PHE*     2.6    71.8    +      +       +      +
    581P  LEU*     3.9     8.5    -      -       +      -
    583P  HIS*     2.5    41.6    +      -       -      -
    588P  VAL*     3.5    36.1    -      -       +      -
    589P  ASP*     1.3    72.3    -      -       -      +
    591P  ASN*     1.3    58.5    +      -       -      +
    592P  ILE*     4.7     0.4    -      -       -      -
    595P  TRP*     4.3     6.3    -      +       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il